Easy Riches
Head behind the potion shop in Kakariko Village to find a grotto. You can catch a fish here. Take as many bottles as you have here and catch the fish. Exit, return and repeat to fill all of your bottles with fish. Take the fish to the beggar in the market at Hyrule Castle and sell them for 100 rupees each. Once you have the Giant's Wallet you can earn as many as 500 rupees this way.
Bonus Bottles
Use a glitch to get as many bottles as you desire. Equip the bottle and then swipe at something you can catch, like a bug or fairy. Press "Start" immediately after catching the item. On the "Pause/Menu" screen equip an item you wish to discard in place of the bottle. Press "Start" to return to the game and your item will be replaced by a bottle while you still have the original bottle in your possession. Be careful not to use this trick with important items or weapons or you may not be able to get them back.
Free Masks
First, sell the Keaton mask to a guard standing outside Death Mountain. Go to the mask shop and ask to borrow the Keaton Mask. Leave the shop and return. Ask to trade the Keaton Mask for the Skull Mask. While the shopkeeper says you must pay for the mask, no rupees will be deducted from your account. You can also use this trick on subsequent masks that you sell to earn more free masks.
Tree House Cow
After winning the horse race at Lon Lon Ranch and earning your horse, Epona, attempt the race again. If you can beat the best time of 49 seconds on the course you will get a cow for your tree house. This will allow you to refill your bottles with life-replenishing milk for free.